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Detailed information for vg0425144906:

Variant ID: vg0425144906 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 25144906
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGCATGTTTAAAAGATCAATATGATGTACACCGACATGTGAATCGAAGTTTTCCCCATATAGCCTTTTTGCTCTATCCAAGCTTTCAGTAATTTGTGT[C/G]
TCAAGGAAGTGTGAATGGTCTTGTTTTGAAGCCTTTCAACACTCAACAGTTCTTGATACAGCTTTCCGTTCTTGTGTATATTTTGCTGGTCCTCCTAGTG

Reverse complement sequence

CACTAGGAGGACCAGCAAAATATACACAAGAACGGAAAGCTGTATCAAGAACTGTTGAGTGTTGAAAGGCTTCAAAACAAGACCATTCACACTTCCTTGA[G/C]
ACACAAATTACTGAAAGCTTGGATAGAGCAAAAAGGCTATATGGGGAAAACTTCGATTCACATGTCGGTGTACATCATATTGATCTTTTAAACATGCAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.80% 0.80% 0.42% 0.00% NA
All Indica  2759 99.50% 0.30% 0.14% 0.00% NA
All Japonica  1512 97.10% 1.90% 0.99% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.30% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.10% 0.38% 0.00% NA
Temperate Japonica  767 94.30% 3.80% 1.96% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0425144906 C -> G LOC_Os04g42480.1 3_prime_UTR_variant ; 255.0bp to feature; MODIFIER silent_mutation Average:75.971; most accessible tissue: Minghui63 flower, score: 85.291 N N N N
vg0425144906 C -> G LOC_Os04g42490.1 downstream_gene_variant ; 971.0bp to feature; MODIFIER silent_mutation Average:75.971; most accessible tissue: Minghui63 flower, score: 85.291 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0425144906 NA 4.83E-06 mr1457_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0425144906 3.50E-06 1.09E-08 mr1458_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251